Choose a pipeline:

From Human Tibia, Sweden SfF11, sample Bone (Tibia) SfF11

Extracted: 40-120 mg of bone was powderized and DNA was extracted with silica-based methods (DOI: 10.1126/science.1253448)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/10.1126/science.1216304)
Repair method:
None
Enrichment method:
PCR

Sequence

Sequenced at:
SNP & SEQ Technology Platform at Uppsala University
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq2000 (chemistry version 3)
Sequencing options:
Default
Output format:
fastq
Quality scale:
Phred 33

Processing

Processed using:
AdapterRemoval/BWA version 1.1/0.5.9
Aligned to:
hg19
Average fold coverage:
0.090x

From Human Teeth, Sweden Gok2, sample Tooth (Teeth) Gok2

Extracted: 40-120 mg of bone was powderized and DNA was extracted with silica-based methods (DOI: 10.1126/science.1253449)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/10.1126/science.1216305)
Repair method:
None
Enrichment method:
PCR

Sequence

Sequenced at:
SNP & SEQ Technology Platform at Uppsala University
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq2000 (chemistry version 3)
Sequencing options:
Default
Output format:
fastq
Quality scale:
Phred 33

Processing

Processed using:
AdapterRemoval/BWA version 1.1/0.5.9
Aligned to:
hg19
Average fold coverage:
1.330x

From Human Teeth, Sweden Gok4, sample Tooth (Teeth) Gok4

Extracted: 40-120 mg of bone was powderized and DNA was extracted with silica-based methods (DOI: 10.1126/science.1253450)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/10.1126/science.1216306)
Repair method:
None
Enrichment method:
PCR

Sequence

Sequenced at:
SNP & SEQ Technology Platform at Uppsala University
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq2000 (chemistry version 3)
Sequencing options:
Default
Output format:
fastq
Quality scale:
Phred 33

Processing

Processed using:
AdapterRemoval/BWA version 1.1/0.5.9
Aligned to:
hg19
Average fold coverage:
0.040x

From Human Teeth, Sweden Gok5, sample Tooth (Teeth) Gok5

Extracted: 40-120 mg of bone was powderized and DNA was extracted with silica-based methods (DOI: 10.1126/science.1253451)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/10.1126/science.1216307)
Repair method:
None
Enrichment method:
PCR

Sequence

Sequenced at:
SNP & SEQ Technology Platform at Uppsala University
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq2000 (chemistry version 3)
Sequencing options:
Default
Output format:
fastq
Quality scale:
Phred 33

Processing

Processed using:
AdapterRemoval/BWA version 1.1/0.5.9
Aligned to:
hg19
Average fold coverage:
0.020x

From Human Teeth, Sweden Gok7, sample Tooth (Teeth) Gok7

Extracted: 40-120 mg of bone was powderized and DNA was extracted with silica-based methods (DOI: 10.1126/science.1253452)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/10.1126/science.1216308)
Repair method:
None
Enrichment method:
PCR

Sequence

Sequenced at:
SNP & SEQ Technology Platform at Uppsala University
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq2000 (chemistry version 3)
Sequencing options:
Default
Output format:
fastq
Quality scale:
Phred 33

Processing

Processed using:
AdapterRemoval/BWA version 1.1/0.5.9
Aligned to:
hg19
Average fold coverage:
0.010x

From Human Cranial fragment, tooth, Sweden Ajv52A, sample Bone (Cranial fragment, tooth) Ajv52A

Extracted: 40-120 mg of bone was powderized and DNA was extracted with silica-based methods (DOI: 10.1126/science.1253453)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/10.1126/science.1216309)
Repair method:
None
Enrichment method:
PCR

Sequence

Sequenced at:
SNP & SEQ Technology Platform at Uppsala University
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq2000 (chemistry version 3)
Sequencing options:
Default
Output format:
fastq
Quality scale:
Phred 33

Processing

Processed using:
AdapterRemoval/BWA version 1.1/0.5.9
Aligned to:
hg19
Average fold coverage:
0.090x

From Human Metatarsal V, tooth, Sweden Ajv53, sample Bone (Metatarsal V, tooth) Ajv53

Extracted: 40-120 mg of bone was powderized and DNA was extracted with silica-based methods (DOI: 10.1126/science.1253454)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/10.1126/science.1216310)
Repair method:
None
Enrichment method:
PCR

Sequence

Sequenced at:
SNP & SEQ Technology Platform at Uppsala University
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq2000 (chemistry version 3)
Sequencing options:
Default
Output format:
fastq
Quality scale:
Phred 33

Processing

Processed using:
AdapterRemoval/BWA version 1.1/0.5.9
Aligned to:
hg19
Average fold coverage:
0.030x

From Human Metatarsal V, tooth, Sweden Ajv58, sample Bone (Metatarsal V, tooth) Ajv58

Extracted: 40-120 mg of bone was powderized and DNA was extracted with silica-based methods (DOI: 10.1126/science.1253455)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/10.1126/science.1216311)
Repair method:
None
Enrichment method:
PCR

Sequence

Sequenced at:
SNP & SEQ Technology Platform at Uppsala University
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq2000 (chemistry version 3)
Sequencing options:
Default
Output format:
fastq
Quality scale:
Phred 33

Processing

Processed using:
AdapterRemoval/BWA version 1.1/0.5.9
Aligned to:
hg19
Average fold coverage:
2.220x

From Human Metatarsal V, tooth, Sweden Ajv59, sample Bone (Metatarsal V, tooth) Ajv59

Extracted: 40-120 mg of bone was powderized and DNA was extracted with silica-based methods (DOI: 10.1126/science.1253456)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/10.1126/science.1216312)
Repair method:
None
Enrichment method:
PCR

Sequence

Sequenced at:
SNP & SEQ Technology Platform at Uppsala University
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq2000 (chemistry version 3)
Sequencing options:
Default
Output format:
fastq
Quality scale:
Phred 33

Processing

Processed using:
AdapterRemoval/BWA version 1.1/0.5.9
Aligned to:
hg19
Average fold coverage:
0.010x

From Human Teeth, Sweden Ajv70, sample Tooth (Teeth) Ajv70

Extracted: 40-120 mg of bone was powderized and DNA was extracted with silica-based methods (DOI: 10.1126/science.1253457)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/10.1126/science.1216313)
Repair method:
None
Enrichment method:
PCR

Sequence

Sequenced at:
SNP & SEQ Technology Platform at Uppsala University
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq2000 (chemistry version 3)
Sequencing options:
Default
Output format:
fastq
Quality scale:
Phred 33

Processing

Processed using:
AdapterRemoval/BWA version 1.1/0.5.9
Aligned to:
hg19
Average fold coverage:
0.160x

From Human Teeth, Sweden Ire8, sample Tooth (Teeth) Ire8

Extracted: 40-120 mg of bone was powderized and DNA was extracted with silica-based methods (DOI: 10.1126/science.1253458)

Library

Type of material:
Genomic
Layout:
Paired
Type of library:
Shotgun
Construction:
(http://dx.doi.org/10.1126/science.1216314)
Repair method:
None
Enrichment method:
PCR

Sequence

Sequenced at:
SNP & SEQ Technology Platform at Uppsala University
Sequencing method:
WGS (Whole genome shotgun sequencing)
Sequencer used:
Illumina HiSeq2000 (chemistry version 3)
Sequencing options:
Default
Output format:
fastq
Quality scale:
Phred 33

Processing

Processed using:
AdapterRemoval/BWA version 1.1/0.5.9
Aligned to:
hg19
Average fold coverage:
0.040x

Analysis

Analysed using samtools/bcftools version 1.2

Please cite as

Skoglund, Pontus; Malmström, Helena; Omrak, Ayça; Raghavan, Maanasa; Valdiosera, Cristina; Günther, Torsten; Hall, Per; Tambets, Kristiina; Parik, Jüri; Sjögren, Karl-Göran; Apel, Jan; Willerslev, Eske; Storå, Jan; Götherström, Anders; Jakobsson, Mattias (2014): Skoglund_scandinavians. Online Ancient Genome Repository. Dataset. http://dx.doi.org/10.4225/55/5781988BB4CEB

Other Studies

This dataset doesn't appear in any other studies.

41 Files

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